rs243725

Variant names:

• chr21-27766613-T-A
• rs243725

Your query was ambiguous. Multiple possible variants found:

• chr21-27766613-T-A
• chr21-27766613-T-C
• chr21-27766613-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.803 in 152,074 control chromosomes in the GnomAD database, including 49,156 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.80 (49156 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121963 AN: 151956 Hom.: 49123 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.781

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.803 AC: 122050 AN: 152074 Hom.: 49156 Cov.: 31 AF XY: 0.803 AC XY: 59650 AN XY: 74312

African (AFR) AF: 0.758 AC: 31458 AN: 41490

American (AMR) AF: 0.796 AC: 12142 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2951 AN: 3470

East Asian (EAS) AF: 0.655 AC: 3358 AN: 5130

South Asian (SAS) AF: 0.831 AC: 4007 AN: 4824

European-Finnish (FIN) AF: 0.848 AC: 8981 AN: 10588

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56634 AN: 67998

Other (OTH) AF: 0.784 AC: 1654 AN: 2110

Alfa AF: 0.824 Hom.: 6436

Bravo AF: 0.791

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.70
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs243725; hg19: chr21-29138932;